No doubt, he was the child of Lucrecia and Hojo, the two assistant scientists in the Jenova Project. But, when Lucrecia was pregnant, Hojo decided he would inject her with Jenova cells so that she would give birth to a child with powers of the Cetra.

It is for this reason, that I don't think you're giving Sephiroth enough credit. By the time Cloud got to the 1 vs. 1 battle with Sephiroth, Sephiroth was already greatly wounded from the three previous battles. It can be agreed that Jenova was the puppet master of this whole game, but that shouldn't take anything away from the fact that Sephiroth was a super-SOLDIER injected with Jenova cells, and mutated using Mako Reactor Number One into an extremely efficient fighting machine. Even before the Mako contaminated him, the game clearly shows his destructive power when fighting Dragons and destroying the entire city of Midgar just to take Jenova out of the Mako Reactors in the mountains.

He is not this little welp that was manipulated by some fraud. Jenova is a planet destroying virus that could easily manipulate anyone and anything it encounters.